SMTL ID : 6dzh.2 (2 other biounits)

HRAS G13D bound to GDP (H13GDP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 20 residues within 4Å: Chain A: A.11, D.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, E.31, D.33, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.3, CA.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.11, A:D.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:D.30, A:E.31, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Water bridges: A:K.16, A:K.16, A:E.31 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.108, G.138, H.166 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.138, H2O.1, H2O.1, H2O.1, H2O.2 MG.3: 3 residues within 4Å: Chain A: S.17, D.33 Ligands: GDP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, A:D.33, H2O.1, H2O.3, H2O.3

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 3 residues within 4Å: Chain A: D.13, D.33 Ligands: GDP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.13, A:D.33

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.5: 2 residues within 4Å: Chain A: T.124, Q.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnson, C.W. et al., Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D. Cell Rep (2019)

Release Date

2019-07-10

Peptides

GTPase HRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTPase HRas

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